GADD45A binds R-loops and recruits TET1 to CpG island promoters

Nat Genet. 2019 Feb;51(2):217-223. doi: 10.1038/s41588-018-0306-6. Epub 2019 Jan 7.

Abstract

R-loops are DNA-RNA hybrids enriched at CpG islands (CGIs) that can regulate chromatin states1-8. How R-loops are recognized and interpreted by specific epigenetic readers is unknown. Here we show that GADD45A (growth arrest and DNA damage protein 45A) binds directly to R-loops and mediates local DNA demethylation by recruiting TET1 (ten-eleven translocation 1). Studying the tumor suppressor TCF21 (ref. 9), we find that antisense long noncoding (lncRNA) TARID (TCF21 antisense RNA inducing promoter demethylation) forms an R-loop at the TCF21 promoter. Binding of GADD45A to the R-loop triggers local DNA demethylation and TCF21 expression. TARID transcription, R-loop formation, DNA demethylation, and TCF21 expression proceed sequentially during the cell cycle. Oxidized DNA demethylation intermediates are enriched at genomic R-loops and their levels increase upon RNase H1 depletion. Genomic profiling in embryonic stem cells identifies thousands of R-loop-dependent TET1 binding sites at CGIs. We propose that GADD45A is an epigenetic R-loop reader that recruits the demethylation machinery to promoter CGIs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Cycle / genetics
  • Cell Cycle Proteins / genetics*
  • Cell Line
  • Chromatin / genetics
  • CpG Islands / genetics*
  • DNA Methylation / genetics
  • DNA-Binding Proteins / genetics
  • Epigenesis, Genetic / genetics
  • Epigenomics / methods
  • HEK293 Cells
  • Humans
  • Mice
  • Mixed Function Oxygenases / genetics*
  • Nuclear Proteins / genetics*
  • Promoter Regions, Genetic / genetics*
  • Protein Binding / genetics
  • Proto-Oncogene Proteins / genetics*
  • RNA, Long Noncoding / genetics
  • Ribonuclease H / genetics
  • Transcription, Genetic / genetics

Substances

  • Cell Cycle Proteins
  • Chromatin
  • DNA-Binding Proteins
  • GADD45A protein, human
  • Nuclear Proteins
  • Proto-Oncogene Proteins
  • RNA, Long Noncoding
  • Mixed Function Oxygenases
  • TET1 protein, human
  • Ribonuclease H
  • ribonuclease HI